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Submission, Monitoring and Control of Jobs

Submission, Monitoring and Control of Jobs. José Luis Vázquez-Poletti (UCM) Training the Trainers (CERN) 16-18 June 2008. Contents. User Model Overview Usage Scenarios Job Definition Commands in detail. STD input STD error STD output. User Model Overview. Performance

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Submission, Monitoring and Control of Jobs

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  1. Submission, Monitoringand Control of Jobs José Luis Vázquez-Poletti (UCM) Training the Trainers (CERN) 16-18 June 2008

  2. Contents User Model Overview Usage Scenarios Job Definition Commands in detail

  3. STD input STD error STD output User Model Overview Performance Profile Job Activity logging Input Files Output Files Application Requirements + Rank Checkpoint Application execution restart Files are architecture independent Application requirements characterization

  4. HOLD MIGRATE PENDING PROLOG WRAPPER EPILOG DONE PRE WRAPPER STOPPED User Model Overview Life-cycle

  5. User Model Overview Main Commands • gwps: Shows job information and state • gwhistory: Shows execution history • gwkill: Sends signals to a job (kill, stop, resume, reschedule)‏ • gwsubmit: Submits a job or array • gwwait: Waits for job's end (any, all, set)‏ • gwuser: User Monitoring • gwhost: Host Monitoring • gwacct: Accounting

  6. Contents User Model Overview Usage Scenarios Job Definition Commands in detail

  7. Usage Scenarios Single Job • Create your proxy. • Create a simple Job Template: • and save it as jt in directory example. • Use gwsubmit command to submit the job: • Use gwhost command to see available resources: • and get more detailed information specifying a Host ID: EXECUTABLE = /bin/ls $ gwsubmit -t example/jt HID PRIO OS ARCH MHZ %CPU MEM(F/T) DISK(F/T) N(U/F/T) LRMS HOSTNAME 0 1 Linux2.6.17-2-6 x86 3216 0 44/2027 76742/118812 0/0/2 Fork cygnus.dacya.ucm.es 1 1 0 0 0/0 0/0 0/0/0 orion.dacya.ucm.es 2 1 Linux2.6.18-4-a x86_6 2211 100 819/1003 77083/77844 0/2/4 PBS hydrus.dacya.ucm.es 3 1 Linux2.6.17-2-6 x86 3216 163 1393/2027 101257/118812 0/2/2 Fork draco.dacya.ucm.es 4 1 Linux2.6.18-4-a x86_6 2211 66 943/1003 72485/77844 0/5/5 SGE aquila.dacya.ucm.es $ gwhost 0 HID PRIO OS ARCH MHZ %CPU MEM(F/T) DISK(F/T) N(U/F/T) LRMS HOSTNAME 0 1 Linux2.6.17-2-6 x86 3216 0 50/2027 76393/118812 0/0/2 Fork cygnus.dacya.ucm.es QUEUENAME SL(F/T) WALLT CPUT COUNT MAXR MAXQ STATUS DISPATCH PRIORITY default 0/2 0 -1 0 -1 0 enabled NULL 0

  8. Usage Scenarios Single Job • Check the resources that match job requirements with gwhost -m 0: • Follow the evolution of the job with gwps command: • HINT: Use gwps -c <seconds> for continuous output. $ gwhost -m 0 HID QNAME RANK PRIO SLOTS HOSTNAME 0 default 0 1 0 cygnus.dacya.ucm.es 2 default 0 1 3 hydrus.dacya.ucm.es 2 qlong 0 1 3 hydrus.dacya.ucm.es 2 qsmall 0 1 3 hydrus.dacya.ucm.es 3 default 0 1 0 draco.dacya.ucm.es 4 all.q 0 1 3 aquila.dacya.ucm.es $ gwps USER JID DM EM START END EXEC XFER EXIT NAME HOST gwtutorial00 0 done ---- 20:16:28 20:18:16 0:00:55 0:00:08 0 stdin aquila.dacya.ucm.es/SGE tinova 1 done ---- 12:26:46 12:31:15 0:03:55 0:00:08 0 stdin hydrus.dacya.ucm.es/PBS tinova 2 pend ---- 12:38:38 --:--:-- 0:00:00 0:00:00 -- t.jt --

  9. Usage Scenarios Single Job • See the job history with gwhistory command: • Once finished... time to retrieve the results: $ gwhistory 4 HID START END PROLOG WRAPPER EPILOG MIGR REASON QUEUE HOST 2 12:58:04 12:58:16 0:00:06 0:00:04 0:00:02 0:00:00 ---- default hydrus.dacya.ucm.es/PBS $ ls -lt stderr.4 stdout.4 -rw-r--r-- 1 tinova tinova 0 2007-09-07 12:58 stderr.4 -rw-r--r-- 1 tinova tinova 72 2007-09-07 12:58 stdout.4 $ cat stdout.4 job.env stderr.execution stderr.wrapper stdout.execution stdout.wrapper

  10. Usage Scenarios Array Jobs • Defining the problem - calculation of the π Number:

  11. Usage Scenarios • pi.c calculates each slice: Examples Directory: $GW_LOCATION/share/examples/ #include <string.h> #include <stdlib.h> int main (int argc, char** args) { int task_id; int total_tasks; long long int n; long long int i; double l_sum, x, h; task_id = atoi(args[1]); total_tasks = atoi(args[2]); n = atoll(args[3]); fprintf(stderr, "task_id=%d total_tasks=%d n=%lld\n", task_id, total_tasks, n); h = 1.0/n; l_sum = 0.0; for (i = task_id; i < n; i += total_tasks) { x = (i + 0.5)*h; l_sum += 4.0/(1.0 + x*x); } l_sum *= h; printf("%0.12g\n", l_sum); return 0; } IMPORTANT 32bits resources: -m32 $ gcc -O3 pi.c -o pi pi arguments: • Task ID • Total tasks • Integral intervals

  12. Usage Scenarios Array Jobs • Create a job template (pi.jt): • Submit the array of jobs: • Use the gwwait command to wait for the jobs: EXECUTABLE = pi ARGUMENTS = $(TASK_ID) $(TOTAL_TASKS) 100000 STDOUT_FILE = stdout_file.$(TASK_ID)‏ STDERR_FILE = stderr_file.$(TASK_ID)‏ RANK = CPU_MHZ $ gwsubmit -v -t pi.jt -n 4 ARRAY ID: 0 TASK JOB 0 3 1 4 2 5 3 6 $ gwwait -v -A 0 0 : 0 1 : 0 2 : 0 3 : 0

  13. Usage Scenarios Array Jobs • At the end we have the following STDOUT files: • Sum the contained values to get the value of π: • IDEA: Embedding all in script? Check the examples directory … stdout_file.0 stdout_file.1 stdout_file.2 stdout_file.3 $ awk 'BEGIN {sum=0} {sum+=$1} END {printf "Pi is %0.12g\n", sum}' stdout_file.* Pi is 3.1415926536

  14. Usage Scenarios Workflow Jobs • GridWay can handle workflows with the following functionality: • Sequence, parallelism, branching and looping structures • The workflow can be described in an abstract form without referring to specific resources for task execution • Quality of service constraints and fault tolerance are defined at task level • Job dependencies specified by using the -d option of the gwsubmit command • $ gwsubmit -v -t A.jt JOB ID: 5 • $ gwsubmit -v -t B.jt -d "5" JOB ID: 6 • $ gwsubmit -v -t C.jt -d "5" JOB ID: 7 • $ gwsubmit -t D.jt -d "6 7"

  15. Contents User Model Overview Usage Scenarios Job Definition Commands in detail

  16. Job Definition Job Template • NAME = Name of the job. Generic Execution • EXECUTABLE=Executable file. • ARGUMENTS=Arguments for the executable. • ENVIRONMENT=User defined, comma-separated, environment variables. • TYPE=“Single”, “multiple” and “mpi” (like GRAM). • NP=Number of processors in MPI jobs. I/O Files • INPUT_FILES=A comma-separated pair of “local remote” filenames. • OUTPUT_FILES=A comma-separated pair of “remote local” filenames.

  17. Job Definition Standard Streams • STDIN_FILE = Standard Input file. • STDOUT_FILE = Standard Output file. • STDERR_FILE = Standard Error file. Check pointing • RESTART_FILES = Checkpoint files, architecture independent. • CHECKPOINT_INTERVAL = Seconds for checkpoint files transfer. • CHECKPOINT_URL = GridFTP URL to store checkpoint files. Resource Selection • REQUIREMENTS = Boolean expression. If true, host will be considered for scheduling. • RANK = Numerical expression evaluated for each host considered for scheduling.

  18. Job Definition Scheduling • RESCHEDULING_INTERVAL = How often GridWay searches better resources for the job. • RESCHEDULING_THRESHOLD = Migration will occur when a better resource is discovered and job is running less than this threshold. • DEADLINE = Deadline of job start. Performance • SUSPENSION_TIMEOUT = Max suspension time in local job management system. • CPULOAD_THRESHOLD = Load threshold for the CPU assigned to job. • MONITOR = Optional program to monitor job performance. Fault Tolerance • RESCHEDULE_ON_FAILURE = Behaviour in case of failure. • NUMBER_OF_RETRIES = Retries in case of failure.

  19. Job Definition • WRAPPER = Script for wrapper. • PRE_WRAPPER = Optional program to be executed before the actual job (i.e. additional remote setup). • PRE_WRAPPER_ARGUMENTS = Arguments for pre-wrapper program. Advanced Job Execution

  20. Job Definition I/O Files • General Syntax: SRC1 DST1, SRC2 DST2,… • Absolute path: EXECUTABLE = /bin/ls • GridFTP URL: INPUT_FILES = gsiftp://machine/tmp/input_exp1 input • File URL: INPUT_FILES = file:///etc/passwd • Name: INPUT_FILES = test_case.bin • NOTE: The source names for output files MUST be a single name, do not use absolute paths or URLs • Any of the above methods except: • STDIN_FILE : Cannot specify a destination name • {STDOUT,STDERR}_FILE : Cannot specify a source name (only destination) Standard Streams

  21. Job Definition Generics • Variables can be used in the value string of each option • with the format: ${GW_VARIABLE} • These variables are substituted at run time with its corresponding value. • For example: STDOUT_FILE = stdout.${JOB_ID} • ${JOB_ID}Job ID. • ${ARRAY_ID}Job array ID. -1 if job is not in any. • ${TASK_ID}Task ID within job array. -1 if job is not in any. • ${ARCH}Architecture of selected execution hosts. • ${PARAM}Allows assignment of arbitrary start and increment values for array jobs (e.g. file naming patterns). • ${MAX_PARAM}Upper bound for the ${PARAM} variable. Valid Variables

  22. Job Definition Resource Selection • Two variables can be used to define valid resources for a given job. • REQUIREMENTS: Express conditions that BAN resources • RANK: Express conditions over the PREFERENCE of resources Rank Requirements

  23. Job Definition Resource Selection • HOSTNAME – FQDN. • ARCH – Architecture of execution host. • OS_NAME – Operative System. • OS_VERSION – Operative System version. • CPU_MODEL – CPU model. • CPU_MHZ – CPU speed in MHZ. • CPU_FREE – Percentage of free CPU. • CPU_SMP – CPU SMP size. • NODECOUNT – Number of nodes. • SIZE_MEM_MB – Memory size in MB. • FREE_MEM_MB – Free memory in MB. • SIZE_DISK_MB – Disk space in MB.

  24. Job Definition Resource Selection • FREE_DISK_MB – Free disk space in MB. • LRMS_NAME – Name of local DRM system. • LRMS_TYPE – Type of local DRM system. • QUEUE_NAME – Name of the queue. • QUEUE_NODECOUNT – Number of queue nodes. • QUEUE_FREENODECOUNT – Free queue nodes. • QUEUE_MAXTIME – Max wall time for jobs in queue. • QUEUE_MAXCPUTIME – Max CPU time of jobs in queue. • QUEUE_MAXCOUNT – Max jobs that can be submitted in one request. • QUEUE_MAXRUNNINGJOBS – Max running jobs in queue. • QUEUE_MAXJOBSINQUEUE – Max queued jobs in queue. • QUEUE_DISPATCHTYPE – Queue dispatch type. • QUEUE_PRIORITY – Priority of queue. • QUEUE_STATUS – Status of queue (i.e. “active”, “production”).

  25. Job Definition Job Environment • GW_RESTARTED • GW_EXECUTABLE • GW_ARCH • GW_CPU_MHZ • GW_MEM_MB • GW_RESTART_FILES • GW_CPULOAD_THRESHOLD • GW_ARGUMENTS • GW_TASK_ID • GW_CPU_MODEL • Job environment variables can be set with the ENVIRONMENT parameter. • The variables defined in the ENVIRONMENT are "sourced" in a bash shell • ENVIRONMENT = VAR = "`expr ${JOB_ID} + 3`" # will set VAR to JOB_ID + 3 • GW_ARRAY_ID • GW_TOTAL_TASKS • GW_JOB_ID • GW_OUTPUT_FILES • GW_INPUT_FILES • GW_OS_NAME • GW_USER • GW_DISK_MB • GW_OS_VERSION

  26. Contents User Model Overview Usage Scenarios Job Definition Commands in detail

  27. Commands in detail gwsubmit – submitting jobs • OPTIONS • -h - Prints help. • -t <template> - The template file describing the job. • -n <tasks> - Submit an array job with the given number of tasks. • All the jobs in the array will use the same template. • -s <start> - Start value for custom param in array jobs. Default 0. • -i <increment> - Increment value for custom param in array jobs • Each task has associated the value PARAM=start+increment * TASK_ID, and MAX_PARM = start+increment*(tasks-1). Default 1. • -d <"id1 id2..."> - Job dependencies. • Submit the job on hold state, and release it once jobs with id1,id2,.. have successfully finished. • -v - Print to stdout the job ids returned by gwd. • -o - Hold job on submission. • -p <priority> - Initial priority for the job. gwsubmit <-t template> [-n tasks] [-h] [-v] [-o] [-s start] \ [-i increment] [-d "id1 id2 ..."]

  28. Commands in detail gwps – monitoring jobs • OPTIONS • -h - Prints help. • -u user - Monitor only jobs owned by user. • -r host - Monitor only jobs executed in host. • -A AID - Monitor only jobs part of the array AID. • -s job_state - Monitor only jobs in states matching that of job_state. • -o output_format - Formats output information, allowing the selection of which fields to display. • -c <delay> - This will cause gwps to print job information every <delay> seconds continuously (similar to top command). • -n - Do not print the header. • job_id - Only monitor this job_id. gwps [-h] [-u user] [-r host] [-A AID] [-s job_state] \ [-o output_format] [-c delay] [-n] [job_id]

  29. Commands in detail gwhistory – accesing job history • OPTIONS • -h - Prints help. • -n - Do not print the header lines. • job_id - Job identification as provided by gwps. gwhistory [-h] [-n] <job_id>

  30. Commands in detail gwhost – monitoring hosts • OPTIONS • -h - Prints help. • -c <delay> - This will cause gwhost to print job information every <delay> seconds continuously (similar to top command). • -n - Do not print the header. • -f - Full format. • -m <job_id> - Prints hosts matching the requirements of a given job. • host_id - Only monitor this host_id, also prints queue information. gwhost [-h] [-c delay] [-nf] [-m job_id] [host_id]

  31. Commands in detail gwkill – signalling jobs • OPTIONS • -h - Prints help. • -a - Asynchronous signal, only relevant for KILL and STOP. • -k - Kill (default, if no signal specified). • -t - Stop job. • -r - Resume job. • -o - Hold job. • -l - Release job. • -s - Re-schedule job. • -9 - Hard kill, removes the job from the system without synchronizing remote job execution or cleaning remote host. • job_id [job_id2 ...] - Job identification as provided by gwps. You can specify a blank space separated list of job ids. • -A <array_id> - Array identification as provided by gwps. gwkill [-h] [-a] [-k | -t | -o | -s | -r | -l | -9] <job_id \ [job_id2 ...] | -A array_id>

  32. Commands in detail gwwait – waiting for jobs • OPTIONS • -h - Prints help. • -a - Any, returns when the first job of the list or array finishes. • -v - Prints job exit code. • -k - Keep jobs, they remain in fail or done states in the GridWay system. • By default, jobs are killed and their resources freed. • -A <array_id> - Array identification as provided by gwps. • job_id ... - Job ids list (blank space separated). gwwait [-h] [-a] [-v] [-k] <job_id...| -A array_id>

  33. Commands in detail gwuser – accesing user information • OPTIONS • -h - Prints help. • -n - Do not print the header. gwuser [-h] [-n]

  34. Commands in detail gwacct – accessing accounting information • OPTIONS • -h - Prints help. • -n - Do not print the header. • <-d n | -w n | -m n | -t s> - Take into account jobs submitted after certain date • specified in number of days (-d), weeks (-w), months (-m) or an epoch (-t). • -u user - Print usage statistics for user. • -r hostname - Print usage statistics for host. gwacct [-h] [-n] [<-d n | -w n | -m n | -t s>]\ <-u user|-r host>

  35. Thank you for your attention!

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